Validator does not check annotationProperty bindings #82

src/dosdp/validator.py

@@ -200,6 +200,31 @@ def test_multi_clause_multi_list(pattern):
     return stat
 
 
+def test_annotation_properties(pattern):
+    """
+    Structurally tests whether an annotation property is declared before use.
+     Args:
+         pattern: schema in yaml format to validate
+
+    Returns: True if all used annotation properties are declared, False otherwise.
+    """
+    declared_annotations = set()
+    if 'annotationProperties' in pattern.keys(): declared_annotations.update(set(pattern['annotationProperties'].keys()))
+    expr = parse('annotations.[*].annotationProperty')
+    used_annotations = [match for match in expr.find(pattern)]
+
+    print(declared_annotations)
+    stat = True
+    if used_annotations:
+        for annotation_prop in used_annotations:
+            val = annotation_prop.value
+            print(val)
+            if val not in declared_annotations:
+                warnings.warn("Annotation property '%s' didn't declared before use." % val)
+                stat = False
+    return stat
+
+
 def format_warning(message, category, filename, lineno, line=None):
     return '%s:%s: %s:%s\n' % (filename, lineno, category.__name__, message)
 
@@ -249,6 +274,7 @@ def validate(pattern):
                 if not test_clause_nesting(pattern): stat = False
                 if not test_axiom_separator(pattern): stat = False
                 if not test_multi_clause_multi_list(pattern): stat = False
+                if not test_annotation_properties(pattern): stat = False
             except YAMLError as exc:
                 stat = False
                 logging.error('Failed to load pattern file: ' + pattern_doc)

src/schema/test/generic_test/validator_test.py

@@ -28,6 +28,8 @@
                                                         "../negative_test_set/multi_clause_with_multi_list.yaml")
 NEGATIVE_PATTERN_MULTI_CLAUSE_MULTI_LIST2 = os.path.join(os.path.dirname(os.path.realpath(__file__)),
                                                          "../negative_test_set/multi_clause_with_multi_list2.yaml")
+NEGATIVE_PATTERN_UNDECLARED_ANNOT_PROP = os.path.join(os.path.dirname(os.path.realpath(__file__)),
+                                                      "../negative_test_set/undeclared_annotation_prop.yaml")
 
 
 class ValidatorTest(unittest.TestCase):
@@ -60,3 +62,6 @@ def test_axiom_separator(self):
     def test_single_list_per_multi_clause(self):
         self.assertFalse(validate(NEGATIVE_PATTERN_MULTI_CLAUSE_MULTI_LIST))
         self.assertFalse(validate(NEGATIVE_PATTERN_MULTI_CLAUSE_MULTI_LIST2))
+
+    def test_undeclared_annotation_prop(self):
+        self.assertFalse(validate(NEGATIVE_PATTERN_UNDECLARED_ANNOT_PROP))

src/schema/test/negative_test_set/undeclared_annotation_prop.yaml

@@ -0,0 +1,47 @@
+pattern_name: acute
+
+pattern_iri: http://purl.obolibrary.org/obo/mondo/patterns/acute.yaml
+
+description: 'This pattern is applied to diseases that are described as having an acute onset, i.e. the sudden appearance of disease manifestations over a short period of time.
+
+Examples: [acute bronchiolitis](http://purl.obolibrary.org/obo/MONDO_0020680),
+  [acute liver failure](http://purl.obolibrary.org/obo/MONDO_0019542)'
+
+contributors:
+- https://orcid.org/0000-0002-6601-2165
+- https://orcid.org/0000-0001-5208-3432
+
+classes:
+  acute: PATO:0000389
+  disease: MONDO:0000001
+
+relations:
+  has modifier: RO:0002573
+
+annotationProperties:
+#  exact_synonym: oio:hasExactSynonym
+  related_synonym: oio:hasRelatedSynonym
+
+vars:
+  disease: '''disease'''
+
+name:
+  text: acute %s
+  vars:
+  - disease
+
+annotations:
+- annotationProperty: exact_synonym
+  text: '%s, acute'
+  vars:
+  - disease
+
+def:
+  text: Acute form of %s.
+  vars:
+  - disease
+
+equivalentTo:
+  text: '%s and ''has modifier'' some ''acute'''
+  vars:
+  - disease